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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1809 by gezelter, Mon Nov 5 19:41:28 2012 UTC vs.
Revision 2033 by gezelter, Sat Nov 1 14:12:16 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 58 | Line 57
57   #include "primitives/Torsion.hpp"
58   #include "primitives/Inversion.hpp"
59   #include "nonbonded/NonBondedInteraction.hpp"
60 < #include "perturbations/ElectricField.hpp"
60 > #include "perturbations/UniformField.hpp"
61   #include "parallel/ForceMatrixDecomposition.hpp"
62  
63   #include <cstdio>
# 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  
376 –
377 –
378 –  
397    void ForceManager::initialize() {
398  
399      if (!info_->isTopologyDone()) {
# Line 384 | Line 402 | namespace OpenMD {
402        interactionMan_->setSimInfo(info_);
403        interactionMan_->initialize();
404  
405 <      // We want to delay the cutoffs until after the interaction
406 <      // manager has set up the atom-atom interactions so that we can
407 <      // query them for suggested cutoff values
405 >      //! We want to delay the cutoffs until after the interaction
406 >      //! manager has set up the atom-atom interactions so that we can
407 >      //! query them for suggested cutoff values
408        setupCutoffs();
409  
410        info_->prepareTopology();      
# 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 +      doSitePotential_ = info_->getSimParams()->getOutputSitePotential();
418    
419      }
420  
421      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
422      
423 <    // Force fields can set options on how to scale van der Waals and
424 <    // electrostatic interactions for atoms connected via bonds, bends
425 <    // and torsions in this case the topological distance between
426 <    // atoms is:
427 <    // 0 = topologically unconnected
428 <    // 1 = bonded together
429 <    // 2 = connected via a bend
430 <    // 3 = connected via a torsion
423 >    //! Force fields can set options on how to scale van der Waals and
424 >    //! electrostatic interactions for atoms connected via bonds, bends
425 >    //! and torsions in this case the topological distance between
426 >    //! atoms is:
427 >    //! 0 = topologically unconnected
428 >    //! 1 = bonded together
429 >    //! 2 = connected via a bend
430 >    //! 3 = connected via a torsion
431      
432      vdwScale_.reserve(4);
433      fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
# Line 424 | Line 445 | namespace OpenMD {
445      electrostaticScale_[2] = fopts.getelectrostatic13scale();
446      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
447      
448 <    if (info_->getSimParams()->haveElectricField()) {
449 <      ElectricField* eField = new ElectricField(info_);
448 >    if (info_->getSimParams()->haveUniformField()) {
449 >      UniformField* eField = new UniformField(info_);
450        perturbations_.push_back(eField);
451      }
452  
453 +    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
454 +    
455      fDecomp_->distributeInitialData();
456 <
456 >    
457      initialized_ = true;
458 <
458 >    
459    }
460 <
460 >  
461    void ForceManager::calcForces() {
462      
463      if (!initialized_) initialize();
464 <
464 >    
465      preCalculation();  
466      shortRangeInteractions();
467      longRangeInteractions();
# Line 612 | Line 635 | namespace OpenMD {
635      // Collect from all nodes.  This should eventually be moved into a
636      // SystemDecomposition, but this is a better place than in
637      // Thermo to do the collection.
638 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
639 <                              MPI::SUM);
640 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
641 <                              MPI::SUM);
642 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
643 <                              MPI::REALTYPE, MPI::SUM);
644 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
645 <                              MPI::REALTYPE, MPI::SUM);
638 >
639 >    MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
640 >                  MPI_SUM, MPI_COMM_WORLD);
641 >    MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
642 >                  MPI_SUM, MPI_COMM_WORLD);
643 >    MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
644 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
645 >    MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
646 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
647   #endif
648  
649      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
# Line 637 | Line 661 | namespace OpenMD {
661    
662    void ForceManager::longRangeInteractions() {
663  
640 –
664      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
665      DataStorage* config = &(curSnapshot->atomData);
666      DataStorage* cgConfig = &(curSnapshot->cgData);
667  
668 +
669      //calculate the center of mass of cutoff group
670  
671      SimInfo::MoleculeIterator mi;
# Line 674 | Line 698 | namespace OpenMD {
698      RealType vij;
699      Vector3d fij, fg, f1;
700      tuple3<RealType, RealType, RealType> cuts;
701 <    RealType rCutSq;
701 >    RealType rCut, rCutSq, rListSq;
702      bool in_switching_region;
703      RealType sw, dswdr, swderiv;
704 <    vector<int> atomListColumn, atomListRow, atomListLocal;
704 >    vector<int> atomListColumn, atomListRow;
705      InteractionData idat;
706      SelfData sdat;
707      RealType mf;
708      RealType vpair;
709      RealType dVdFQ1(0.0);
710      RealType dVdFQ2(0.0);
687 –    Vector3d eField1(0.0);
688 –    Vector3d eField2(0.0);
711      potVec longRangePotential(0.0);
712 +    RealType reciprocalPotential(0.0);
713      potVec workPot(0.0);
714      potVec exPot(0.0);
715 +    Vector3d eField1(0.0);
716 +    Vector3d eField2(0.0);
717 +    RealType sPot1(0.0);
718 +    RealType sPot2(0.0);
719 +                  
720      vector<int>::iterator ia, jb;
721  
722      int loopStart, loopEnd;
723 <
723 >    
724 >    idat.rcut = &rCut;
725      idat.vdwMult = &vdwMult;
726      idat.electroMult = &electroMult;
727      idat.pot = &workPot;
# Line 703 | Line 732 | namespace OpenMD {
732      idat.dVdFQ1 = &dVdFQ1;
733      idat.dVdFQ2 = &dVdFQ2;
734      idat.eField1 = &eField1;
735 <    idat.eField2 = &eField2;
735 >    idat.eField2 = &eField2;
736 >    idat.sPot1 = &sPot1;
737 >    idat.sPot2 = &sPot2;
738      idat.f1 = &f1;
739      idat.sw = &sw;
740      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
741 <    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
741 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE ||
742 >                         cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
743      idat.doParticlePot = doParticlePot_;
744 +    idat.doElectricField = doElectricField_;
745 +    idat.doSitePotential = doSitePotential_;
746      sdat.doParticlePot = doParticlePot_;
747      
748      loopEnd = PAIR_LOOP;
# Line 721 | Line 755 | namespace OpenMD {
755      
756        if (iLoop == loopStart) {
757          bool update_nlist = fDecomp_->checkNeighborList();
758 <        if (update_nlist)
759 <          neighborList = fDecomp_->buildNeighborList();
760 <      }            
758 >        if (update_nlist) {
759 >          if (!usePeriodicBoundaryConditions_)
760 >            Mat3x3d bbox = thermo->getBoundingBox();
761 >          fDecomp_->buildNeighborList(neighborList_);
762 >        }
763 >      }
764  
765 <      for (vector<pair<int, int> >::iterator it = neighborList.begin();
766 <             it != neighborList.end(); ++it) {
765 >      for (vector<pair<int, int> >::iterator it = neighborList_.begin();
766 >           it != neighborList_.end(); ++it) {
767                  
768          cg1 = (*it).first;
769          cg2 = (*it).second;
770          
771 <        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
771 >        fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq);
772  
773          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
774  
775 <        curSnapshot->wrapVector(d_grp);        
775 >        // already wrapped in the getIntergroupVector call:
776 >        // curSnapshot->wrapVector(d_grp);        
777          rgrpsq = d_grp.lengthSquare();
740 –        rCutSq = cuts.second;
778  
779          if (rgrpsq < rCutSq) {
743 –          idat.rcut = &cuts.first;
780            if (iLoop == PAIR_LOOP) {
781              vij = 0.0;
782 <            fij = V3Zero;
782 >            fij.zero();
783 >            eField1.zero();
784 >            eField2.zero();
785 >            sPot1 = 0.0;
786 >            sPot2 = 0.0;
787            }
788            
789            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
# Line 768 | Line 808 | namespace OpenMD {
808                  vpair = 0.0;
809                  workPot = 0.0;
810                  exPot = 0.0;
811 <                f1 = V3Zero;
811 >                f1.zero();
812                  dVdFQ1 = 0.0;
813                  dVdFQ2 = 0.0;
814  
# Line 795 | Line 835 | namespace OpenMD {
835                
836                  r = sqrt( *(idat.r2) );
837                  idat.rij = &r;
838 <              
838 >
839                  if (iLoop == PREPAIR_LOOP) {
840                    interactionMan_->doPrePair(idat);
841                  } else {
# Line 891 | Line 931 | namespace OpenMD {
931          }
932        }
933      }
934 <  
934 >    
935      // collects pairwise information
936      fDecomp_->collectData();
937 +    if (cutoffMethod_ == EWALD_FULL) {
938 +      interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
939 +
940 +      curSnapshot->setReciprocalPotential(reciprocalPotential);
941 +    }
942          
943      if (info_->requiresSelfCorrection()) {
944        for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
# Line 911 | Line 956 | namespace OpenMD {
956      curSnapshot->setLongRangePotential(longRangePotential);
957      
958      curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
959 <                                         *(fDecomp_->getExcludedPotential()));
959 >                                       *(fDecomp_->getExcludedPotential()));
960  
961    }
962  
918 –  
963    void ForceManager::postCalculation() {
964  
965      vector<Perturbation*>::iterator pi;
# Line 941 | Line 985 | namespace OpenMD {
985      }
986      
987   #ifdef IS_MPI
988 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
989 <                              MPI::REALTYPE, MPI::SUM);
988 >    MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
989 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
990   #endif
991      curSnapshot->setStressTensor(stressTensor);
992      
993 +    if (info_->getSimParams()->getUseLongRangeCorrections()) {
994 +      /*
995 +        RealType vol = curSnapshot->getVolume();
996 +        RealType Elrc(0.0);
997 +        RealType Wlrc(0.0);
998 +
999 +        set<AtomType*>::iterator i;
1000 +        set<AtomType*>::iterator j;
1001 +    
1002 +        RealType n_i, n_j;
1003 +        RealType rho_i, rho_j;
1004 +        pair<RealType, RealType> LRI;
1005 +      
1006 +        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
1007 +        n_i = RealType(info_->getGlobalCountOfType(*i));
1008 +        rho_i = n_i /  vol;
1009 +        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
1010 +        n_j = RealType(info_->getGlobalCountOfType(*j));
1011 +        rho_j = n_j / vol;
1012 +          
1013 +        LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1014 +
1015 +        Elrc += n_i   * rho_j * LRI.first;
1016 +        Wlrc -= rho_i * rho_j * LRI.second;
1017 +        }
1018 +        }
1019 +        Elrc *= 2.0 * NumericConstant::PI;
1020 +        Wlrc *= 2.0 * NumericConstant::PI;
1021 +
1022 +        RealType lrp = curSnapshot->getLongRangePotential();
1023 +        curSnapshot->setLongRangePotential(lrp + Elrc);
1024 +        stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1025 +        curSnapshot->setStressTensor(stressTensor);
1026 +      */
1027 +    
1028 +    }
1029    }
1030 < } //end namespace OpenMD
1030 > }

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