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Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 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 >                                               initialized_(false) {
72      forceField_ = info_->getForceField();
73      interactionMan_ = new InteractionManager();
74      fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75 +    thermo = new Thermo(info_);
76    }
77  
78 +  ForceManager::~ForceManager() {
79 +    perturbations_.clear();
80 +    
81 +    delete switcher_;
82 +    delete interactionMan_;
83 +    delete fDecomp_;
84 +    delete thermo;
85 +  }
86 +  
87    /**
88     * setupCutoffs
89     *
# Line 117 | Line 128 | namespace OpenMD {
128      else
129        mdFileVersion = 0;
130    
131 +    // We need the list of simulated atom types to figure out cutoffs
132 +    // as well as long range corrections.
133 +
134 +    set<AtomType*>::iterator i;
135 +    set<AtomType*> atomTypes_;
136 +    atomTypes_ = info_->getSimulatedAtomTypes();
137 +
138      if (simParams_->haveCutoffRadius()) {
139        rCut_ = simParams_->getCutoffRadius();
140      } else {      
# Line 131 | Line 149 | namespace OpenMD {
149          rCut_ = 12.0;
150        } else {
151          RealType thisCut;
152 <        set<AtomType*>::iterator i;
135 <        set<AtomType*> atomTypes;
136 <        atomTypes = info_->getSimulatedAtomTypes();        
137 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
152 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
153            thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
154            rCut_ = max(thisCut, rCut_);
155          }
# Line 369 | Line 384 | namespace OpenMD {
384      }
385      switcher_->setSwitchType(sft_);
386      switcher_->setSwitch(rSwitch_, rCut_);
372 –    interactionMan_->setSwitchingRadius(rSwitch_);
387    }
388  
389  
# Line 393 | Line 407 | namespace OpenMD {
407        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
408        doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
409        if (doHeatFlux_) doParticlePot_ = true;
410 +
411 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
412    
413      }
414  
# Line 423 | Line 439 | namespace OpenMD {
439      electrostaticScale_[2] = fopts.getelectrostatic13scale();
440      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
441      
442 <    fDecomp_->distributeInitialData();
443 <
444 <    initialized_ = true;
442 >    if (info_->getSimParams()->haveElectricField()) {
443 >      ElectricField* eField = new ElectricField(info_);
444 >      perturbations_.push_back(eField);
445 >    }
446  
447 +    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
448 +    
449 +    fDecomp_->distributeInitialData();
450 +    
451 +    initialized_ = true;
452 +    
453    }
454 <
454 >  
455    void ForceManager::calcForces() {
456      
457      if (!initialized_) initialize();
458 <
458 >    
459      preCalculation();  
460      shortRangeInteractions();
461      longRangeInteractions();
# Line 671 | Line 694 | namespace OpenMD {
694      RealType rCutSq;
695      bool in_switching_region;
696      RealType sw, dswdr, swderiv;
697 <    vector<int> atomListColumn, atomListRow, atomListLocal;
697 >    vector<int> atomListColumn, atomListRow;
698      InteractionData idat;
699      SelfData sdat;
700      RealType mf;
678 –    RealType lrPot;
701      RealType vpair;
702      RealType dVdFQ1(0.0);
703      RealType dVdFQ2(0.0);
704      potVec longRangePotential(0.0);
705      potVec workPot(0.0);
706      potVec exPot(0.0);
707 +    Vector3d eField1(0.0);
708 +    Vector3d eField2(0.0);
709      vector<int>::iterator ia, jb;
710  
711      int loopStart, loopEnd;
# Line 695 | Line 719 | namespace OpenMD {
719      idat.vpair = &vpair;
720      idat.dVdFQ1 = &dVdFQ1;
721      idat.dVdFQ2 = &dVdFQ2;
722 +    idat.eField1 = &eField1;
723 +    idat.eField2 = &eField2;  
724      idat.f1 = &f1;
725      idat.sw = &sw;
726      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
727      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
728      idat.doParticlePot = doParticlePot_;
729 +    idat.doElectricField = doElectricField_;
730      sdat.doParticlePot = doParticlePot_;
731      
732      loopEnd = PAIR_LOOP;
# Line 712 | Line 739 | namespace OpenMD {
739      
740        if (iLoop == loopStart) {
741          bool update_nlist = fDecomp_->checkNeighborList();
742 <        if (update_nlist)
742 >        if (update_nlist) {
743 >          if (!usePeriodicBoundaryConditions_)
744 >            Mat3x3d bbox = thermo->getBoundingBox();
745            neighborList = fDecomp_->buildNeighborList();
746 <      }            
746 >        }
747 >      }
748  
749        for (vector<pair<int, int> >::iterator it = neighborList.begin();
750               it != neighborList.end(); ++it) {
# Line 735 | Line 765 | namespace OpenMD {
765            if (iLoop == PAIR_LOOP) {
766              vij = 0.0;
767              fij = V3Zero;
768 +            eField1 = V3Zero;
769 +            eField2 = V3Zero;
770            }
771            
772            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
# Line 809 | Line 841 | namespace OpenMD {
841                fij += fg;
842  
843                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
844 <                stressTensor -= outProduct( *(idat.d), fg);
845 <                if (doHeatFlux_)
846 <                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
847 <                
844 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
845 >                                            atomListColumn[0],
846 >                                            cg1, cg2)) {
847 >                  stressTensor -= outProduct( *(idat.d), fg);
848 >                  if (doHeatFlux_)
849 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
850 >                }                
851                }
852            
853                for (ia = atomListRow.begin();
# Line 869 | Line 904 | namespace OpenMD {
904  
905            fDecomp_->collectIntermediateData();
906  
907 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
907 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
908              fDecomp_->fillSelfData(sdat, atom1);
909              interactionMan_->doPreForce(sdat);
910            }
# Line 884 | Line 919 | namespace OpenMD {
919      fDecomp_->collectData();
920          
921      if (info_->requiresSelfCorrection()) {
922 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
922 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
923          fDecomp_->fillSelfData(sdat, atom1);
924          interactionMan_->doSelfCorrection(sdat);
925        }
# Line 897 | Line 932 | namespace OpenMD {
932        *(fDecomp_->getPairwisePotential());
933  
934      curSnapshot->setLongRangePotential(longRangePotential);
900 –
901 –    // lrPot = longRangePotential.sum();
902 –
903 –    // //store the long range potential  
904 –    // curSnapshot->setLongRangePotential(lrPot);
935      
936      curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
937                                           *(fDecomp_->getExcludedPotential()));
# Line 910 | Line 940 | namespace OpenMD {
940  
941    
942    void ForceManager::postCalculation() {
943 +
944 +    vector<Perturbation*>::iterator pi;
945 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
946 +      (*pi)->applyPerturbation();
947 +    }
948 +
949      SimInfo::MoleculeIterator mi;
950      Molecule* mol;
951      Molecule::RigidBodyIterator rbIter;
# Line 933 | Line 969 | namespace OpenMD {
969   #endif
970      curSnapshot->setStressTensor(stressTensor);
971      
972 <  }
972 >    if (info_->getSimParams()->getUseLongRangeCorrections()) {
973 >      /*
974 >      RealType vol = curSnapshot->getVolume();
975 >      RealType Elrc(0.0);
976 >      RealType Wlrc(0.0);
977  
978 < } //end namespace OpenMD
978 >      set<AtomType*>::iterator i;
979 >      set<AtomType*>::iterator j;
980 >    
981 >      RealType n_i, n_j;
982 >      RealType rho_i, rho_j;
983 >      pair<RealType, RealType> LRI;
984 >      
985 >      for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
986 >        n_i = RealType(info_->getGlobalCountOfType(*i));
987 >        rho_i = n_i /  vol;
988 >        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
989 >          n_j = RealType(info_->getGlobalCountOfType(*j));
990 >          rho_j = n_j / vol;
991 >          
992 >          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
993 >
994 >          Elrc += n_i   * rho_j * LRI.first;
995 >          Wlrc -= rho_i * rho_j * LRI.second;
996 >        }
997 >      }
998 >      Elrc *= 2.0 * NumericConstant::PI;
999 >      Wlrc *= 2.0 * NumericConstant::PI;
1000 >
1001 >      RealType lrp = curSnapshot->getLongRangePotential();
1002 >      curSnapshot->setLongRangePotential(lrp + Elrc);
1003 >      stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1004 >      curSnapshot->setStressTensor(stressTensor);
1005 >      */
1006 >    
1007 >    }
1008 >  }
1009 > }

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