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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1808 by gezelter, Mon Oct 22 20:42:10 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 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 429 | Line 443 | namespace OpenMD {
443        perturbations_.push_back(eField);
444      }
445  
446 <    fDecomp_->distributeInitialData();
447 <
448 <    initialized_ = true;
449 <
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 722 | 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 745 | 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 819 | 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 907 | Line 931 | namespace OpenMD {
931        *(fDecomp_->getPairwisePotential());
932  
933      curSnapshot->setLongRangePotential(longRangePotential);
910 –
911 –    // collects single-atom information
912 –    fDecomp_->collectSelfData();
913 –
914 –    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
915 –      *(fDecomp_->getPairwisePotential());
916 –
917 –    curSnapshot->setLongRangePotential(longRangePotential);
934      
935      curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
936                                           *(fDecomp_->getExcludedPotential()));
# Line 952 | Line 968 | namespace OpenMD {
968   #endif
969      curSnapshot->setStressTensor(stressTensor);
970      
971 +    if (info_->getSimParams()->getUseLongRangeCorrections()) {
972 +      /*
973 +      RealType vol = curSnapshot->getVolume();
974 +      RealType Elrc(0.0);
975 +      RealType Wlrc(0.0);
976 +
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 < } //end namespace OpenMD
1008 > }

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