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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 1850 by gezelter, Wed Feb 20 15:39:39 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 117 | Line 117 | namespace OpenMD {
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 131 | Line 138 | namespace OpenMD {
138          rCut_ = 12.0;
139        } else {
140          RealType thisCut;
141 <        set<AtomType*>::iterator i;
135 <        set<AtomType*> atomTypes;
136 <        atomTypes = info_->getSimulatedAtomTypes();        
137 <        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 745 | 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,
# Line 819 | 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 907 | Line 916 | namespace OpenMD {
916        *(fDecomp_->getPairwisePotential());
917  
918      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);
919      
920      curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
921                                           *(fDecomp_->getExcludedPotential()));
# Line 952 | Line 953 | namespace OpenMD {
953   #endif
954      curSnapshot->setStressTensor(stressTensor);
955      
956 +    if (info_->getSimParams()->getUseLongRangeCorrections()) {
957 +      /*
958 +      RealType vol = curSnapshot->getVolume();
959 +      RealType Elrc(0.0);
960 +      RealType Wlrc(0.0);
961 +
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 < } //end namespace OpenMD
993 > }

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