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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1788 by gezelter, Wed Aug 29 20:17:07 2012 UTC vs.
Revision 1893 by gezelter, Wed Jun 19 17:19:07 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 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,
101 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
102     *                        or SHIFTED_POTENTIAL)
103     *      If cutoffMethod was explicitly set, use that choice.
104     *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
# 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    
176      if (simParams_->haveCutoffMethod()) {
177        string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
# Line 166 | Line 181 | namespace OpenMD {
181          sprintf(painCave.errMsg,
182                  "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
183                  "\tShould be one of: "
184 <                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
184 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
185 >                "\tor SHIFTED_FORCE\n",
186                  cutMeth.c_str());
187          painCave.isFatal = 1;
188          painCave.severity = OPENMD_ERROR;
# Line 210 | Line 226 | namespace OpenMD {
226              cutoffMethod_ = SHIFTED_POTENTIAL;
227            } else if (myMethod == "SHIFTED_FORCE") {
228              cutoffMethod_ = SHIFTED_FORCE;
229 +          } else if (myMethod == "TAYLOR_SHIFTED") {
230 +            cutoffMethod_ = TAYLOR_SHIFTED;
231            }
232          
233            if (simParams_->haveSwitchingRadius())
234              rSwitch_ = simParams_->getSwitchingRadius();
235  
236 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
236 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
237 >              myMethod == "TAYLOR_SHIFTED") {
238              if (simParams_->haveSwitchingRadius()){
239                sprintf(painCave.errMsg,
240                        "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
# Line 370 | Line 389 | namespace OpenMD {
389      }
390      switcher_->setSwitchType(sft_);
391      switcher_->setSwitch(rSwitch_, rCut_);
373 –    interactionMan_->setSwitchingRadius(rSwitch_);
392    }
393  
394  
# Line 394 | Line 412 | namespace OpenMD {
412        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
413        doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
414        if (doHeatFlux_) doParticlePot_ = true;
415 +
416 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
417    
418      }
419  
# Line 429 | Line 449 | namespace OpenMD {
449        perturbations_.push_back(eField);
450      }
451  
452 +    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
453 +    
454      fDecomp_->distributeInitialData();
455 <
455 >    
456      initialized_ = true;
457 <
457 >    
458    }
459 <
459 >  
460    void ForceManager::calcForces() {
461      
462      if (!initialized_) initialize();
463 <
463 >    
464      preCalculation();  
465      shortRangeInteractions();
466      longRangeInteractions();
# Line 637 | Line 659 | namespace OpenMD {
659    
660    void ForceManager::longRangeInteractions() {
661  
640 –
662      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
663      DataStorage* config = &(curSnapshot->atomData);
664      DataStorage* cgConfig = &(curSnapshot->cgData);
# Line 677 | Line 698 | namespace OpenMD {
698      RealType rCutSq;
699      bool in_switching_region;
700      RealType sw, dswdr, swderiv;
701 <    vector<int> atomListColumn, atomListRow, atomListLocal;
701 >    vector<int> atomListColumn, atomListRow;
702      InteractionData idat;
703      SelfData sdat;
704      RealType mf;
705      RealType vpair;
706      RealType dVdFQ1(0.0);
707      RealType dVdFQ2(0.0);
687 –    Vector3d eField1(0.0);
688 –    Vector3d eField2(0.0);
708      potVec longRangePotential(0.0);
709      potVec workPot(0.0);
710      potVec exPot(0.0);
711 +    Vector3d eField1(0.0);
712 +    Vector3d eField2(0.0);
713      vector<int>::iterator ia, jb;
714  
715      int loopStart, loopEnd;
# Line 703 | Line 724 | namespace OpenMD {
724      idat.dVdFQ1 = &dVdFQ1;
725      idat.dVdFQ2 = &dVdFQ2;
726      idat.eField1 = &eField1;
727 <    idat.eField2 = &eField2;
727 >    idat.eField2 = &eField2;  
728      idat.f1 = &f1;
729      idat.sw = &sw;
730      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
731 <    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
731 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
732      idat.doParticlePot = doParticlePot_;
733 +    idat.doElectricField = doElectricField_;
734      sdat.doParticlePot = doParticlePot_;
735      
736      loopEnd = PAIR_LOOP;
# Line 721 | Line 743 | namespace OpenMD {
743      
744        if (iLoop == loopStart) {
745          bool update_nlist = fDecomp_->checkNeighborList();
746 <        if (update_nlist)
746 >        if (update_nlist) {
747 >          if (!usePeriodicBoundaryConditions_)
748 >            Mat3x3d bbox = thermo->getBoundingBox();
749            neighborList = fDecomp_->buildNeighborList();
750 <      }            
750 >        }
751 >      }
752  
753        for (vector<pair<int, int> >::iterator it = neighborList.begin();
754               it != neighborList.end(); ++it) {
# Line 735 | Line 760 | namespace OpenMD {
760  
761          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
762  
763 <        curSnapshot->wrapVector(d_grp);        
763 >        // already wrapped in the getIntergroupVector call:
764 >        // curSnapshot->wrapVector(d_grp);        
765          rgrpsq = d_grp.lengthSquare();
766          rCutSq = cuts.second;
767  
# Line 743 | Line 769 | namespace OpenMD {
769            idat.rcut = &cuts.first;
770            if (iLoop == PAIR_LOOP) {
771              vij = 0.0;
772 <            fij = V3Zero;
772 >            fij.zero();
773 >            eField1.zero();
774 >            eField2.zero();
775            }
776            
777            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
# Line 768 | Line 796 | namespace OpenMD {
796                  vpair = 0.0;
797                  workPot = 0.0;
798                  exPot = 0.0;
799 <                f1 = V3Zero;
799 >                f1.zero();
800                  dVdFQ1 = 0.0;
801                  dVdFQ2 = 0.0;
802  
# Line 818 | Line 846 | namespace OpenMD {
846                fij += fg;
847  
848                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
849 <                stressTensor -= outProduct( *(idat.d), fg);
850 <                if (doHeatFlux_)
851 <                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
852 <                
849 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
850 >                                            atomListColumn[0],
851 >                                            cg1, cg2)) {
852 >                  stressTensor -= outProduct( *(idat.d), fg);
853 >                  if (doHeatFlux_)
854 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
855 >                }                
856                }
857            
858                for (ia = atomListRow.begin();
# Line 888 | Line 919 | namespace OpenMD {
919          }
920        }
921      }
922 <  
922 >    
923      // collects pairwise information
924      fDecomp_->collectData();
925          
# Line 943 | Line 974 | namespace OpenMD {
974   #endif
975      curSnapshot->setStressTensor(stressTensor);
976      
977 +    if (info_->getSimParams()->getUseLongRangeCorrections()) {
978 +      /*
979 +      RealType vol = curSnapshot->getVolume();
980 +      RealType Elrc(0.0);
981 +      RealType Wlrc(0.0);
982 +
983 +      set<AtomType*>::iterator i;
984 +      set<AtomType*>::iterator j;
985 +    
986 +      RealType n_i, n_j;
987 +      RealType rho_i, rho_j;
988 +      pair<RealType, RealType> LRI;
989 +      
990 +      for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
991 +        n_i = RealType(info_->getGlobalCountOfType(*i));
992 +        rho_i = n_i /  vol;
993 +        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
994 +          n_j = RealType(info_->getGlobalCountOfType(*j));
995 +          rho_j = n_j / vol;
996 +          
997 +          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
998 +
999 +          Elrc += n_i   * rho_j * LRI.first;
1000 +          Wlrc -= rho_i * rho_j * LRI.second;
1001 +        }
1002 +      }
1003 +      Elrc *= 2.0 * NumericConstant::PI;
1004 +      Wlrc *= 2.0 * NumericConstant::PI;
1005 +
1006 +      RealType lrp = curSnapshot->getLongRangePotential();
1007 +      curSnapshot->setLongRangePotential(lrp + Elrc);
1008 +      stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1009 +      curSnapshot->setStressTensor(stressTensor);
1010 +      */
1011 +    
1012 +    }
1013    }
1014 < } //end namespace OpenMD
1014 > }

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