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Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
Revision 1868 by gezelter, Tue Apr 30 15:56:54 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 67 | Line 67 | namespace OpenMD {
67   using namespace std;
68   namespace OpenMD {
69    
70 <  ForceManager::ForceManager(SimInfo * info) : info_(info) {
70 >  ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL) {
71      forceField_ = info_->getForceField();
72      interactionMan_ = new InteractionManager();
73      fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74 +    thermo = new Thermo(info_);
75    }
76  
77 +  ForceManager::~ForceManager() {
78 +    perturbations_.clear();
79 +    
80 +    delete switcher_;
81 +    delete interactionMan_;
82 +    delete fDecomp_;
83 +    delete thermo;
84 +  }
85 +  
86    /**
87     * setupCutoffs
88     *
# Line 110 | Line 120 | namespace OpenMD {
120      Globals* simParams_ = info_->getSimParams();
121      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
122      int mdFileVersion;
123 +    rCut_ = 0.0; //Needs a value for a later max() call;  
124      
125      if (simParams_->haveMDfileVersion())
126        mdFileVersion = simParams_->getMDfileVersion();
127      else
128        mdFileVersion = 0;
129    
130 +    // We need the list of simulated atom types to figure out cutoffs
131 +    // as well as long range corrections.
132 +
133 +    set<AtomType*>::iterator i;
134 +    set<AtomType*> atomTypes_;
135 +    atomTypes_ = info_->getSimulatedAtomTypes();
136 +
137      if (simParams_->haveCutoffRadius()) {
138        rCut_ = simParams_->getCutoffRadius();
139      } else {      
# Line 130 | Line 148 | namespace OpenMD {
148          rCut_ = 12.0;
149        } else {
150          RealType thisCut;
151 <        set<AtomType*>::iterator i;
134 <        set<AtomType*> atomTypes;
135 <        atomTypes = info_->getSimulatedAtomTypes();        
136 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
151 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
152            thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
153            rCut_ = max(thisCut, rCut_);
154          }
# Line 368 | Line 383 | namespace OpenMD {
383      }
384      switcher_->setSwitchType(sft_);
385      switcher_->setSwitch(rSwitch_, rCut_);
371 –    interactionMan_->setSwitchingRadius(rSwitch_);
386    }
387  
388  
# Line 392 | Line 406 | namespace OpenMD {
406        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
407        doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
408        if (doHeatFlux_) doParticlePot_ = true;
409 +
410 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
411    
412      }
413  
# Line 422 | Line 438 | namespace OpenMD {
438      electrostaticScale_[2] = fopts.getelectrostatic13scale();
439      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
440      
441 +    if (info_->getSimParams()->haveElectricField()) {
442 +      ElectricField* eField = new ElectricField(info_);
443 +      perturbations_.push_back(eField);
444 +    }
445 +
446 +    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
447 +    
448      fDecomp_->distributeInitialData();
449 <
449 >    
450      initialized_ = true;
451 <
451 >    
452    }
453 <
453 >  
454    void ForceManager::calcForces() {
455      
456      if (!initialized_) initialize();
457 <
457 >    
458      preCalculation();  
459      shortRangeInteractions();
460      longRangeInteractions();
# Line 448 | Line 471 | namespace OpenMD {
471      Molecule::CutoffGroupIterator ci;
472      CutoffGroup* cg;
473      
474 <    // forces are zeroed here, before any are accumulated.
474 >    // forces and potentials are zeroed here, before any are
475 >    // accumulated.
476      
477 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
478 +
479 +    snap->setBondPotential(0.0);
480 +    snap->setBendPotential(0.0);
481 +    snap->setTorsionPotential(0.0);
482 +    snap->setInversionPotential(0.0);
483 +
484 +    potVec zeroPot(0.0);
485 +    snap->setLongRangePotential(zeroPot);
486 +    snap->setExcludedPotentials(zeroPot);
487 +
488 +    snap->setRestraintPotential(0.0);
489 +    snap->setRawPotential(0.0);
490 +
491      for (mol = info_->beginMolecule(mi); mol != NULL;
492           mol = info_->nextMolecule(mi)) {
493        for(atom = mol->beginAtom(ai); atom != NULL;
# Line 475 | Line 513 | namespace OpenMD {
513      // Zero out the stress tensor
514      stressTensor *= 0.0;
515      // Zero out the heatFlux
516 <    fDecomp_->setHeatFlux( V3Zero );    
516 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
517    }
518    
519    void ForceManager::shortRangeInteractions() {
# Line 585 | Line 623 | namespace OpenMD {
623          }      
624        }      
625      }
626 <    
627 <    RealType  shortRangePotential = bondPotential + bendPotential +
628 <      torsionPotential +  inversionPotential;    
626 >
627 > #ifdef IS_MPI
628 >    // Collect from all nodes.  This should eventually be moved into a
629 >    // SystemDecomposition, but this is a better place than in
630 >    // Thermo to do the collection.
631 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
632 >                              MPI::SUM);
633 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
634 >                              MPI::SUM);
635 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
636 >                              MPI::REALTYPE, MPI::SUM);
637 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
638 >                              MPI::REALTYPE, MPI::SUM);
639 > #endif
640 >
641      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
642 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
643 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
644 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
645 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
646 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
642 >
643 >    curSnapshot->setBondPotential(bondPotential);
644 >    curSnapshot->setBendPotential(bendPotential);
645 >    curSnapshot->setTorsionPotential(torsionPotential);
646 >    curSnapshot->setInversionPotential(inversionPotential);
647 >    
648 >    // RealType shortRangePotential = bondPotential + bendPotential +
649 >    //   torsionPotential +  inversionPotential;    
650 >
651 >    // curSnapshot->setShortRangePotential(shortRangePotential);
652    }
653    
654    void ForceManager::longRangeInteractions() {
# Line 642 | Line 697 | namespace OpenMD {
697      InteractionData idat;
698      SelfData sdat;
699      RealType mf;
645 –    RealType lrPot;
700      RealType vpair;
701 +    RealType dVdFQ1(0.0);
702 +    RealType dVdFQ2(0.0);
703      potVec longRangePotential(0.0);
704      potVec workPot(0.0);
705 +    potVec exPot(0.0);
706 +    Vector3d eField1(0.0);
707 +    Vector3d eField2(0.0);
708      vector<int>::iterator ia, jb;
709  
710      int loopStart, loopEnd;
# Line 653 | Line 712 | namespace OpenMD {
712      idat.vdwMult = &vdwMult;
713      idat.electroMult = &electroMult;
714      idat.pot = &workPot;
715 +    idat.excludedPot = &exPot;
716      sdat.pot = fDecomp_->getEmbeddingPotential();
717 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
718      idat.vpair = &vpair;
719 +    idat.dVdFQ1 = &dVdFQ1;
720 +    idat.dVdFQ2 = &dVdFQ2;
721 +    idat.eField1 = &eField1;
722 +    idat.eField2 = &eField2;  
723      idat.f1 = &f1;
724      idat.sw = &sw;
725      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
726      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
727      idat.doParticlePot = doParticlePot_;
728 +    idat.doElectricField = doElectricField_;
729      sdat.doParticlePot = doParticlePot_;
730      
731      loopEnd = PAIR_LOOP;
# Line 668 | Line 734 | namespace OpenMD {
734      } else {
735        loopStart = PAIR_LOOP;
736      }
671 –  
737      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
738      
739        if (iLoop == loopStart) {
740          bool update_nlist = fDecomp_->checkNeighborList();
741 <        if (update_nlist)
741 >        if (update_nlist) {
742 >          if (!usePeriodicBoundaryConditions_)
743 >            Mat3x3d bbox = thermo->getBoundingBox();
744            neighborList = fDecomp_->buildNeighborList();
745 <      }            
745 >        }
746 >      }
747  
748        for (vector<pair<int, int> >::iterator it = neighborList.begin();
749               it != neighborList.end(); ++it) {
# Line 696 | Line 764 | namespace OpenMD {
764            if (iLoop == PAIR_LOOP) {
765              vij = 0.0;
766              fij = V3Zero;
767 +            eField1 = V3Zero;
768 +            eField2 = V3Zero;
769            }
770            
771            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
772                                                       rgrp);
773 <          
773 >
774            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
775            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
776  
777            if (doHeatFlux_)
778              gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
779 <        
779 >
780            for (ia = atomListRow.begin();
781                 ia != atomListRow.end(); ++ia) {            
782              atom1 = (*ia);
783 <            
783 >
784              for (jb = atomListColumn.begin();
785                   jb != atomListColumn.end(); ++jb) {              
786                atom2 = (*jb);
787  
788 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
788 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
789 >
790                  vpair = 0.0;
791                  workPot = 0.0;
792 +                exPot = 0.0;
793                  f1 = V3Zero;
794 +                dVdFQ1 = 0.0;
795 +                dVdFQ2 = 0.0;
796  
797                  fDecomp_->fillInteractionData(idat, atom1, atom2);
798 <                
798 >
799                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
800                  vdwMult = vdwScale_[topoDist];
801                  electroMult = electrostaticScale_[topoDist];
# Line 766 | Line 840 | namespace OpenMD {
840                fij += fg;
841  
842                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
843 <                stressTensor -= outProduct( *(idat.d), fg);
844 <                if (doHeatFlux_)
845 <                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
846 <                
843 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
844 >                                            atomListColumn[0],
845 >                                            cg1, cg2)) {
846 >                  stressTensor -= outProduct( *(idat.d), fg);
847 >                  if (doHeatFlux_)
848 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
849 >                }                
850                }
851            
852                for (ia = atomListRow.begin();
# Line 826 | Line 903 | namespace OpenMD {
903  
904            fDecomp_->collectIntermediateData();
905  
906 <          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_->doPreForce(sdat);
909            }
# Line 837 | Line 914 | namespace OpenMD {
914        }
915      }
916      
917 +    // collects pairwise information
918      fDecomp_->collectData();
919          
920      if (info_->requiresSelfCorrection()) {
921 <
844 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
921 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
922          fDecomp_->fillSelfData(sdat, atom1);
923          interactionMan_->doSelfCorrection(sdat);
924        }
848 –
925      }
926  
927 +    // collects single-atom information
928 +    fDecomp_->collectSelfData();
929 +
930      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
931        *(fDecomp_->getPairwisePotential());
932  
933 <    lrPot = longRangePotential.sum();
933 >    curSnapshot->setLongRangePotential(longRangePotential);
934 >    
935 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
936 >                                         *(fDecomp_->getExcludedPotential()));
937  
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];
938    }
939  
940    
941    void ForceManager::postCalculation() {
942 +
943 +    vector<Perturbation*>::iterator pi;
944 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
945 +      (*pi)->applyPerturbation();
946 +    }
947 +
948      SimInfo::MoleculeIterator mi;
949      Molecule* mol;
950      Molecule::RigidBodyIterator rbIter;
951      RigidBody* rb;
952      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
953 <    
953 >  
954      // collect the atomic forces onto rigid bodies
955      
956      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 879 | Line 963 | namespace OpenMD {
963      }
964      
965   #ifdef IS_MPI
882 –
966      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
967                                MPI::REALTYPE, MPI::SUM);
968   #endif
969      curSnapshot->setStressTensor(stressTensor);
970      
971 <  }
971 >    if (info_->getSimParams()->getUseLongRangeCorrections()) {
972 >      /*
973 >      RealType vol = curSnapshot->getVolume();
974 >      RealType Elrc(0.0);
975 >      RealType Wlrc(0.0);
976  
977 < } //end namespace OpenMD
977 >      set<AtomType*>::iterator i;
978 >      set<AtomType*>::iterator j;
979 >    
980 >      RealType n_i, n_j;
981 >      RealType rho_i, rho_j;
982 >      pair<RealType, RealType> LRI;
983 >      
984 >      for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
985 >        n_i = RealType(info_->getGlobalCountOfType(*i));
986 >        rho_i = n_i /  vol;
987 >        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
988 >          n_j = RealType(info_->getGlobalCountOfType(*j));
989 >          rho_j = n_j / vol;
990 >          
991 >          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
992 >
993 >          Elrc += n_i   * rho_j * LRI.first;
994 >          Wlrc -= rho_i * rho_j * LRI.second;
995 >        }
996 >      }
997 >      Elrc *= 2.0 * NumericConstant::PI;
998 >      Wlrc *= 2.0 * NumericConstant::PI;
999 >
1000 >      RealType lrp = curSnapshot->getLongRangePotential();
1001 >      curSnapshot->setLongRangePotential(lrp + Elrc);
1002 >      stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1003 >      curSnapshot->setStressTensor(stressTensor);
1004 >      */
1005 >    
1006 >    }
1007 >  }
1008 > }

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