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Revision 1733 by jmichalk, Tue Jun 5 17:48:40 2012 UTC vs.
Revision 1866 by gezelter, Thu Apr 25 14:32:56 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# 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 71 | Line 71 | namespace OpenMD {
71      forceField_ = info_->getForceField();
72      interactionMan_ = new InteractionManager();
73      fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74 +    thermo = new Thermo(info_);
75    }
76  
77    /**
# 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();
118      else
119        mdFileVersion = 0;
120    
121 +    // We need the list of simulated atom types to figure out cutoffs
122 +    // as well as long range corrections.
123 +
124 +    set<AtomType*>::iterator i;
125 +    set<AtomType*> atomTypes_;
126 +    atomTypes_ = info_->getSimulatedAtomTypes();
127 +
128      if (simParams_->haveCutoffRadius()) {
129        rCut_ = simParams_->getCutoffRadius();
130      } else {      
# Line 130 | Line 139 | namespace OpenMD {
139          rCut_ = 12.0;
140        } else {
141          RealType thisCut;
142 <        set<AtomType*>::iterator i;
134 <        set<AtomType*> atomTypes;
135 <        atomTypes = info_->getSimulatedAtomTypes();        
136 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
142 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
143            thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
144            rCut_ = max(thisCut, rCut_);
145          }
# Line 368 | Line 374 | namespace OpenMD {
374      }
375      switcher_->setSwitchType(sft_);
376      switcher_->setSwitch(rSwitch_, rCut_);
371 –    interactionMan_->setSwitchingRadius(rSwitch_);
377    }
378  
379  
# Line 392 | Line 397 | namespace OpenMD {
397        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
398        doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
399        if (doHeatFlux_) doParticlePot_ = true;
400 +
401 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
402    
403      }
404  
# Line 422 | Line 429 | namespace OpenMD {
429      electrostaticScale_[2] = fopts.getelectrostatic13scale();
430      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
431      
432 <    fDecomp_->distributeInitialData();
433 <
434 <    initialized_ = true;
432 >    if (info_->getSimParams()->haveElectricField()) {
433 >      ElectricField* eField = new ElectricField(info_);
434 >      perturbations_.push_back(eField);
435 >    }
436  
437 +    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
438 +    
439 +    fDecomp_->distributeInitialData();
440 +    
441 +    initialized_ = true;
442 +    
443    }
444 <
444 >  
445    void ForceManager::calcForces() {
446      
447      if (!initialized_) initialize();
448 <
448 >    
449      preCalculation();  
450      shortRangeInteractions();
451      longRangeInteractions();
# Line 448 | Line 462 | namespace OpenMD {
462      Molecule::CutoffGroupIterator ci;
463      CutoffGroup* cg;
464      
465 <    // forces are zeroed here, before any are accumulated.
465 >    // forces and potentials are zeroed here, before any are
466 >    // accumulated.
467      
468 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
469 +
470 +    snap->setBondPotential(0.0);
471 +    snap->setBendPotential(0.0);
472 +    snap->setTorsionPotential(0.0);
473 +    snap->setInversionPotential(0.0);
474 +
475 +    potVec zeroPot(0.0);
476 +    snap->setLongRangePotential(zeroPot);
477 +    snap->setExcludedPotentials(zeroPot);
478 +
479 +    snap->setRestraintPotential(0.0);
480 +    snap->setRawPotential(0.0);
481 +
482      for (mol = info_->beginMolecule(mi); mol != NULL;
483           mol = info_->nextMolecule(mi)) {
484        for(atom = mol->beginAtom(ai); atom != NULL;
# Line 475 | Line 504 | namespace OpenMD {
504      // Zero out the stress tensor
505      stressTensor *= 0.0;
506      // Zero out the heatFlux
507 <    fDecomp_->setHeatFlux( V3Zero );    
507 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
508    }
509    
510    void ForceManager::shortRangeInteractions() {
# Line 585 | Line 614 | namespace OpenMD {
614          }      
615        }      
616      }
617 <    
618 <    RealType  shortRangePotential = bondPotential + bendPotential +
619 <      torsionPotential +  inversionPotential;    
617 >
618 > #ifdef IS_MPI
619 >    // Collect from all nodes.  This should eventually be moved into a
620 >    // SystemDecomposition, but this is a better place than in
621 >    // Thermo to do the collection.
622 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
623 >                              MPI::SUM);
624 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
625 >                              MPI::SUM);
626 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
627 >                              MPI::REALTYPE, MPI::SUM);
628 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
629 >                              MPI::REALTYPE, MPI::SUM);
630 > #endif
631 >
632      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
633 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
634 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
635 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
636 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
637 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
633 >
634 >    curSnapshot->setBondPotential(bondPotential);
635 >    curSnapshot->setBendPotential(bendPotential);
636 >    curSnapshot->setTorsionPotential(torsionPotential);
637 >    curSnapshot->setInversionPotential(inversionPotential);
638 >    
639 >    // RealType shortRangePotential = bondPotential + bendPotential +
640 >    //   torsionPotential +  inversionPotential;    
641 >
642 >    // curSnapshot->setShortRangePotential(shortRangePotential);
643    }
644    
645    void ForceManager::longRangeInteractions() {
# Line 642 | Line 688 | namespace OpenMD {
688      InteractionData idat;
689      SelfData sdat;
690      RealType mf;
645 –    RealType lrPot;
691      RealType vpair;
692      RealType dVdFQ1(0.0);
693      RealType dVdFQ2(0.0);
694      potVec longRangePotential(0.0);
695      potVec workPot(0.0);
696 +    potVec exPot(0.0);
697 +    Vector3d eField1(0.0);
698 +    Vector3d eField2(0.0);
699      vector<int>::iterator ia, jb;
700  
701      int loopStart, loopEnd;
# Line 655 | Line 703 | namespace OpenMD {
703      idat.vdwMult = &vdwMult;
704      idat.electroMult = &electroMult;
705      idat.pot = &workPot;
706 +    idat.excludedPot = &exPot;
707      sdat.pot = fDecomp_->getEmbeddingPotential();
708 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
709      idat.vpair = &vpair;
710      idat.dVdFQ1 = &dVdFQ1;
711      idat.dVdFQ2 = &dVdFQ2;
712 +    idat.eField1 = &eField1;
713 +    idat.eField2 = &eField2;  
714      idat.f1 = &f1;
715      idat.sw = &sw;
716      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
717      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
718      idat.doParticlePot = doParticlePot_;
719 +    idat.doElectricField = doElectricField_;
720      sdat.doParticlePot = doParticlePot_;
721      
722      loopEnd = PAIR_LOOP;
# Line 672 | Line 725 | namespace OpenMD {
725      } else {
726        loopStart = PAIR_LOOP;
727      }
675 –  
728      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
729      
730        if (iLoop == loopStart) {
731          bool update_nlist = fDecomp_->checkNeighborList();
732 <        if (update_nlist)
732 >        if (update_nlist) {
733 >          if (!usePeriodicBoundaryConditions_)
734 >            Mat3x3d bbox = thermo->getBoundingBox();
735            neighborList = fDecomp_->buildNeighborList();
736 <      }            
736 >        }
737 >      }
738  
739        for (vector<pair<int, int> >::iterator it = neighborList.begin();
740               it != neighborList.end(); ++it) {
# Line 700 | Line 755 | namespace OpenMD {
755            if (iLoop == PAIR_LOOP) {
756              vij = 0.0;
757              fij = V3Zero;
758 +            eField1 = V3Zero;
759 +            eField2 = V3Zero;
760            }
761            
762            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
763                                                       rgrp);
764 <          
764 >
765            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
766            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
767  
768            if (doHeatFlux_)
769              gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
770 <        
770 >
771            for (ia = atomListRow.begin();
772                 ia != atomListRow.end(); ++ia) {            
773              atom1 = (*ia);
774 <            
774 >
775              for (jb = atomListColumn.begin();
776                   jb != atomListColumn.end(); ++jb) {              
777                atom2 = (*jb);
778  
779 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
779 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
780 >
781                  vpair = 0.0;
782                  workPot = 0.0;
783 +                exPot = 0.0;
784                  f1 = V3Zero;
785                  dVdFQ1 = 0.0;
786                  dVdFQ2 = 0.0;
787  
788                  fDecomp_->fillInteractionData(idat, atom1, atom2);
789 <                
789 >
790                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
791                  vdwMult = vdwScale_[topoDist];
792                  electroMult = electrostaticScale_[topoDist];
# Line 772 | Line 831 | namespace OpenMD {
831                fij += fg;
832  
833                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
834 <                stressTensor -= outProduct( *(idat.d), fg);
835 <                if (doHeatFlux_)
836 <                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
837 <                
834 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
835 >                                            atomListColumn[0],
836 >                                            cg1, cg2)) {
837 >                  stressTensor -= outProduct( *(idat.d), fg);
838 >                  if (doHeatFlux_)
839 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
840 >                }                
841                }
842            
843                for (ia = atomListRow.begin();
# Line 832 | Line 894 | namespace OpenMD {
894  
895            fDecomp_->collectIntermediateData();
896  
897 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
897 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
898              fDecomp_->fillSelfData(sdat, atom1);
899              interactionMan_->doPreForce(sdat);
900            }
# Line 843 | Line 905 | namespace OpenMD {
905        }
906      }
907      
908 +    // collects pairwise information
909      fDecomp_->collectData();
910          
911      if (info_->requiresSelfCorrection()) {
912 <
850 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
912 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
913          fDecomp_->fillSelfData(sdat, atom1);
914          interactionMan_->doSelfCorrection(sdat);
915        }
854 –
916      }
917  
918 +    // collects single-atom information
919 +    fDecomp_->collectSelfData();
920 +
921      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
922        *(fDecomp_->getPairwisePotential());
923  
924 <    lrPot = longRangePotential.sum();
924 >    curSnapshot->setLongRangePotential(longRangePotential);
925 >    
926 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
927 >                                         *(fDecomp_->getExcludedPotential()));
928  
862 –    //store the stressTensor and long range potential    
863 –    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
864 –    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
865 –    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
929    }
930  
931    
932    void ForceManager::postCalculation() {
933 +
934 +    vector<Perturbation*>::iterator pi;
935 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
936 +      (*pi)->applyPerturbation();
937 +    }
938 +
939      SimInfo::MoleculeIterator mi;
940      Molecule* mol;
941      Molecule::RigidBodyIterator rbIter;
942      RigidBody* rb;
943      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
944 <    
944 >  
945      // collect the atomic forces onto rigid bodies
946      
947      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 885 | Line 954 | namespace OpenMD {
954      }
955      
956   #ifdef IS_MPI
888 –
957      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
958                                MPI::REALTYPE, MPI::SUM);
959   #endif
960      curSnapshot->setStressTensor(stressTensor);
961      
962 <  }
962 >    if (info_->getSimParams()->getUseLongRangeCorrections()) {
963 >      /*
964 >      RealType vol = curSnapshot->getVolume();
965 >      RealType Elrc(0.0);
966 >      RealType Wlrc(0.0);
967  
968 < } //end namespace OpenMD
968 >      set<AtomType*>::iterator i;
969 >      set<AtomType*>::iterator j;
970 >    
971 >      RealType n_i, n_j;
972 >      RealType rho_i, rho_j;
973 >      pair<RealType, RealType> LRI;
974 >      
975 >      for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
976 >        n_i = RealType(info_->getGlobalCountOfType(*i));
977 >        rho_i = n_i /  vol;
978 >        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
979 >          n_j = RealType(info_->getGlobalCountOfType(*j));
980 >          rho_j = n_j / vol;
981 >          
982 >          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
983 >
984 >          Elrc += n_i   * rho_j * LRI.first;
985 >          Wlrc -= rho_i * rho_j * LRI.second;
986 >        }
987 >      }
988 >      Elrc *= 2.0 * NumericConstant::PI;
989 >      Wlrc *= 2.0 * NumericConstant::PI;
990 >
991 >      RealType lrp = curSnapshot->getLongRangePotential();
992 >      curSnapshot->setLongRangePotential(lrp + Elrc);
993 >      stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
994 >      curSnapshot->setStressTensor(stressTensor);
995 >      */
996 >    
997 >    }
998 >  }
999 > }

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