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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1987 by gezelter, Thu Apr 17 19:07:31 2014 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 68 | 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 88 | Line 98 | namespace OpenMD {
98     *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
99     *      Use the maximum suggested value that was found.
100     *
101 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
102 <   *                        or SHIFTED_POTENTIAL)
101 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
102 >   *                        SHIFTED_POTENTIAL, or EWALD_FULL)
103     *      If cutoffMethod was explicitly set, use that choice.
104     *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
105     *
# Line 118 | 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 132 | Line 149 | namespace OpenMD {
149          rCut_ = 12.0;
150        } else {
151          RealType thisCut;
152 <        set<AtomType*>::iterator i;
136 <        set<AtomType*> atomTypes;
137 <        atomTypes = info_->getSimulatedAtomTypes();        
138 <        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 157 | Line 171 | namespace OpenMD {
171      stringToCutoffMethod["SWITCHED"] = SWITCHED;
172      stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
173      stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
174 +    stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
175 +    stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL;
176    
177      if (simParams_->haveCutoffMethod()) {
178        string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
# Line 166 | Line 182 | namespace OpenMD {
182          sprintf(painCave.errMsg,
183                  "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
184                  "\tShould be one of: "
185 <                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
185 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
186 >                "\tSHIFTED_FORCE, or EWALD_FULL\n",
187                  cutMeth.c_str());
188          painCave.isFatal = 1;
189          painCave.severity = OPENMD_ERROR;
# Line 210 | Line 227 | namespace OpenMD {
227              cutoffMethod_ = SHIFTED_POTENTIAL;
228            } else if (myMethod == "SHIFTED_FORCE") {
229              cutoffMethod_ = SHIFTED_FORCE;
230 +          } else if (myMethod == "TAYLOR_SHIFTED") {
231 +            cutoffMethod_ = TAYLOR_SHIFTED;
232 +          } else if (myMethod == "EWALD_FULL") {
233 +            cutoffMethod_ = EWALD_FULL;
234            }
235          
236            if (simParams_->haveSwitchingRadius())
237              rSwitch_ = simParams_->getSwitchingRadius();
238  
239 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
239 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
240 >              myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
241              if (simParams_->haveSwitchingRadius()){
242                sprintf(painCave.errMsg,
243                        "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
# Line 370 | Line 392 | namespace OpenMD {
392      }
393      switcher_->setSwitchType(sft_);
394      switcher_->setSwitch(rSwitch_, rCut_);
373 –    interactionMan_->setSwitchingRadius(rSwitch_);
395    }
396  
397  
# Line 394 | Line 415 | namespace OpenMD {
415        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
416        doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
417        if (doHeatFlux_) doParticlePot_ = true;
418 +
419 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
420    
421      }
422  
# Line 429 | Line 452 | namespace OpenMD {
452        perturbations_.push_back(eField);
453      }
454  
455 <    fDecomp_->distributeInitialData();
456 <
455 >    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
456 >    
457 >    fDecomp_->distributeInitialData();
458 >    
459      initialized_ = true;
460 <
460 >    
461    }
462 <
462 >  
463    void ForceManager::calcForces() {
464      
465      if (!initialized_) initialize();
466 <
466 >    
467      preCalculation();  
468      shortRangeInteractions();
469      longRangeInteractions();
# Line 612 | Line 637 | namespace OpenMD {
637      // Collect from all nodes.  This should eventually be moved into a
638      // SystemDecomposition, but this is a better place than in
639      // Thermo to do the collection.
640 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
641 <                              MPI::SUM);
642 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
643 <                              MPI::SUM);
644 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
645 <                              MPI::REALTYPE, MPI::SUM);
646 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
647 <                              MPI::REALTYPE, MPI::SUM);
640 >
641 >    MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
642 >                  MPI_SUM, MPI_COMM_WORLD);
643 >    MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
644 >                  MPI_SUM, MPI_COMM_WORLD);
645 >    MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
646 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
647 >    MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
648 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
649   #endif
650  
651      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
# Line 637 | Line 663 | namespace OpenMD {
663    
664    void ForceManager::longRangeInteractions() {
665  
640 –
666      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
667      DataStorage* config = &(curSnapshot->atomData);
668      DataStorage* cgConfig = &(curSnapshot->cgData);
669  
670 +
671      //calculate the center of mass of cutoff group
672  
673      SimInfo::MoleculeIterator mi;
# Line 674 | Line 700 | namespace OpenMD {
700      RealType vij;
701      Vector3d fij, fg, f1;
702      tuple3<RealType, RealType, RealType> cuts;
703 <    RealType rCutSq;
703 >    RealType rCut, rCutSq, rListSq;
704      bool in_switching_region;
705      RealType sw, dswdr, swderiv;
706 <    vector<int> atomListColumn, atomListRow, atomListLocal;
706 >    vector<int> atomListColumn, atomListRow;
707      InteractionData idat;
708      SelfData sdat;
709      RealType mf;
# Line 685 | Line 711 | namespace OpenMD {
711      RealType dVdFQ1(0.0);
712      RealType dVdFQ2(0.0);
713      potVec longRangePotential(0.0);
714 +    RealType reciprocalPotential(0.0);
715      potVec workPot(0.0);
716      potVec exPot(0.0);
717 +    Vector3d eField1(0.0);
718 +    Vector3d eField2(0.0);
719      vector<int>::iterator ia, jb;
720  
721      int loopStart, loopEnd;
722 <
722 >    
723 >    idat.rcut = &rCut;
724      idat.vdwMult = &vdwMult;
725      idat.electroMult = &electroMult;
726      idat.pot = &workPot;
# Line 700 | Line 730 | namespace OpenMD {
730      idat.vpair = &vpair;
731      idat.dVdFQ1 = &dVdFQ1;
732      idat.dVdFQ2 = &dVdFQ2;
733 +    idat.eField1 = &eField1;
734 +    idat.eField2 = &eField2;  
735      idat.f1 = &f1;
736      idat.sw = &sw;
737      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
738 <    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
738 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
739      idat.doParticlePot = doParticlePot_;
740 +    idat.doElectricField = doElectricField_;
741      sdat.doParticlePot = doParticlePot_;
742      
743      loopEnd = PAIR_LOOP;
# Line 717 | Line 750 | namespace OpenMD {
750      
751        if (iLoop == loopStart) {
752          bool update_nlist = fDecomp_->checkNeighborList();
753 <        if (update_nlist)
754 <          neighborList = fDecomp_->buildNeighborList();
755 <      }            
753 >        if (update_nlist) {
754 >          if (!usePeriodicBoundaryConditions_)
755 >            Mat3x3d bbox = thermo->getBoundingBox();
756 >          fDecomp_->buildNeighborList(neighborList_);
757 >        }
758 >      }
759  
760 <      for (vector<pair<int, int> >::iterator it = neighborList.begin();
761 <             it != neighborList.end(); ++it) {
760 >      for (vector<pair<int, int> >::iterator it = neighborList_.begin();
761 >             it != neighborList_.end(); ++it) {
762                  
763          cg1 = (*it).first;
764          cg2 = (*it).second;
765          
766 <        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
766 >        fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq);
767  
768          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
769  
770 <        curSnapshot->wrapVector(d_grp);        
770 >        // already wrapped in the getIntergroupVector call:
771 >        // curSnapshot->wrapVector(d_grp);        
772          rgrpsq = d_grp.lengthSquare();
736 –        rCutSq = cuts.second;
773  
774          if (rgrpsq < rCutSq) {
739 –          idat.rcut = &cuts.first;
775            if (iLoop == PAIR_LOOP) {
776              vij = 0.0;
777 <            fij = V3Zero;
777 >            fij.zero();
778 >            eField1.zero();
779 >            eField2.zero();
780            }
781            
782            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
# Line 764 | Line 801 | namespace OpenMD {
801                  vpair = 0.0;
802                  workPot = 0.0;
803                  exPot = 0.0;
804 <                f1 = V3Zero;
804 >                f1.zero();
805                  dVdFQ1 = 0.0;
806                  dVdFQ2 = 0.0;
807  
# Line 791 | Line 828 | namespace OpenMD {
828                
829                  r = sqrt( *(idat.r2) );
830                  idat.rij = &r;
831 <              
831 >
832                  if (iLoop == PREPAIR_LOOP) {
833                    interactionMan_->doPrePair(idat);
834                  } else {
# Line 814 | Line 851 | namespace OpenMD {
851                fij += fg;
852  
853                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
854 <                stressTensor -= outProduct( *(idat.d), fg);
855 <                if (doHeatFlux_)
856 <                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
857 <                
854 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
855 >                                            atomListColumn[0],
856 >                                            cg1, cg2)) {
857 >                  stressTensor -= outProduct( *(idat.d), fg);
858 >                  if (doHeatFlux_)
859 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
860 >                }                
861                }
862            
863                for (ia = atomListRow.begin();
# Line 884 | Line 924 | namespace OpenMD {
924          }
925        }
926      }
927 <  
927 >    
928      // collects pairwise information
929      fDecomp_->collectData();
930 +    if (cutoffMethod_ == EWALD_FULL) {
931 +      interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
932 +
933 +      curSnapshot->setReciprocalPotential(reciprocalPotential);
934 +    }
935          
936      if (info_->requiresSelfCorrection()) {
937        for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
# Line 908 | Line 953 | namespace OpenMD {
953  
954    }
955  
911 –  
956    void ForceManager::postCalculation() {
957  
958      vector<Perturbation*>::iterator pi;
# Line 934 | Line 978 | namespace OpenMD {
978      }
979      
980   #ifdef IS_MPI
981 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
982 <                              MPI::REALTYPE, MPI::SUM);
981 >    MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
982 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
983   #endif
984      curSnapshot->setStressTensor(stressTensor);
985      
986 +    if (info_->getSimParams()->getUseLongRangeCorrections()) {
987 +      /*
988 +      RealType vol = curSnapshot->getVolume();
989 +      RealType Elrc(0.0);
990 +      RealType Wlrc(0.0);
991 +
992 +      set<AtomType*>::iterator i;
993 +      set<AtomType*>::iterator j;
994 +    
995 +      RealType n_i, n_j;
996 +      RealType rho_i, rho_j;
997 +      pair<RealType, RealType> LRI;
998 +      
999 +      for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
1000 +        n_i = RealType(info_->getGlobalCountOfType(*i));
1001 +        rho_i = n_i /  vol;
1002 +        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
1003 +          n_j = RealType(info_->getGlobalCountOfType(*j));
1004 +          rho_j = n_j / vol;
1005 +          
1006 +          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1007 +
1008 +          Elrc += n_i   * rho_j * LRI.first;
1009 +          Wlrc -= rho_i * rho_j * LRI.second;
1010 +        }
1011 +      }
1012 +      Elrc *= 2.0 * NumericConstant::PI;
1013 +      Wlrc *= 2.0 * NumericConstant::PI;
1014 +
1015 +      RealType lrp = curSnapshot->getLongRangePotential();
1016 +      curSnapshot->setLongRangePotential(lrp + Elrc);
1017 +      stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1018 +      curSnapshot->setStressTensor(stressTensor);
1019 +      */
1020 +    
1021 +    }
1022    }
1023 < } //end namespace OpenMD
1023 > }

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