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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1760 by gezelter, Thu Jun 21 19:26:46 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 117 | Line 127 | namespace OpenMD {
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 131 | Line 148 | namespace OpenMD {
148          rCut_ = 12.0;
149        } else {
150          RealType thisCut;
151 <        set<AtomType*>::iterator i;
135 <        set<AtomType*> atomTypes;
136 <        atomTypes = info_->getSimulatedAtomTypes();        
137 <        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 369 | Line 383 | namespace OpenMD {
383      }
384      switcher_->setSwitchType(sft_);
385      switcher_->setSwitch(rSwitch_, rCut_);
372 –    interactionMan_->setSwitchingRadius(rSwitch_);
386    }
387  
388  
# Line 393 | 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 423 | Line 438 | namespace OpenMD {
438      electrostaticScale_[2] = fopts.getelectrostatic13scale();
439      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
440      
441 <    fDecomp_->distributeInitialData();
442 <
443 <    initialized_ = true;
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 +    
450 +    initialized_ = true;
451 +    
452    }
453 <
453 >  
454    void ForceManager::calcForces() {
455      
456      if (!initialized_) initialize();
457 <
457 >    
458      preCalculation();  
459      shortRangeInteractions();
460      longRangeInteractions();
# Line 449 | 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 608 | Line 645 | namespace OpenMD {
645      curSnapshot->setTorsionPotential(torsionPotential);
646      curSnapshot->setInversionPotential(inversionPotential);
647      
648 <    RealType shortRangePotential = bondPotential + bendPotential +
649 <      torsionPotential +  inversionPotential;    
648 >    // RealType shortRangePotential = bondPotential + bendPotential +
649 >    //   torsionPotential +  inversionPotential;    
650  
651 <    curSnapshot->setShortRangePotential(shortRangePotential);
651 >    // curSnapshot->setShortRangePotential(shortRangePotential);
652    }
653    
654    void ForceManager::longRangeInteractions() {
# Line 660 | Line 697 | namespace OpenMD {
697      InteractionData idat;
698      SelfData sdat;
699      RealType mf;
663 –    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 676 | Line 714 | namespace OpenMD {
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 696 | Line 738 | namespace OpenMD {
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 719 | 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,
# Line 793 | 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 853 | 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 868 | Line 918 | namespace OpenMD {
918      fDecomp_->collectData();
919          
920      if (info_->requiresSelfCorrection()) {
921 <      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        }
# Line 880 | Line 930 | namespace OpenMD {
930      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
931        *(fDecomp_->getPairwisePotential());
932  
933 <    curSnapshot->setLongRangePotentialFamilies(longRangePotential);
933 >    curSnapshot->setLongRangePotential(longRangePotential);
934 >    
935 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
936 >                                         *(fDecomp_->getExcludedPotential()));
937  
885 –    lrPot = longRangePotential.sum();
886 –
887 –    //store the long range potential  
888 –    curSnapshot->setLongRangePotential(lrPot);
889 –
890 –    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedPotential()));
891 –
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 916 | Line 968 | namespace OpenMD {
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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