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root/OpenMD/trunk/src/brains/ForceManager.cpp
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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC vs.
Revision 2033 by gezelter, Sat Nov 1 14:12:16 2014 UTC

# Line 57 | 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 99 | Line 99 | namespace OpenMD {
99     *      Use the maximum suggested value that was found.
100     *
101     * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
102 <   *                        or SHIFTED_POTENTIAL)
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 172 | Line 172 | namespace OpenMD {
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 182 | Line 183 | namespace OpenMD {
183                  "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
184                  "\tShould be one of: "
185                  "HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
186 <                "\tor SHIFTED_FORCE\n",
186 >                "\tSHIFTED_FORCE, or EWALD_FULL\n",
187                  cutMeth.c_str());
188          painCave.isFatal = 1;
189          painCave.severity = OPENMD_ERROR;
# Line 228 | Line 229 | namespace OpenMD {
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" ||
240 <              myMethod == "TAYLOR_SHIFTED") {
240 >              myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
241              if (simParams_->haveSwitchingRadius()){
242                sprintf(painCave.errMsg,
243                        "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
# Line 391 | Line 394 | namespace OpenMD {
394      switcher_->setSwitch(rSwitch_, rCut_);
395    }
396  
394 –
395 –
396 –  
397    void ForceManager::initialize() {
398  
399      if (!info_->isTopologyDone()) {
# Line 402 | 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 414 | Line 414 | namespace OpenMD {
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 444 | 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  
# Line 634 | 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 663 | Line 665 | namespace OpenMD {
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 695 | 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;
# Line 705 | Line 708 | namespace OpenMD {
708      RealType vpair;
709      RealType dVdFQ1(0.0);
710      RealType dVdFQ2(0.0);
708 –    Vector3d eField1(0.0);
709 –    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 724 | 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 || cutoffMethod_ == TAYLOR_SHIFTED) ? 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 746 | Line 758 | namespace OpenMD {
758          if (update_nlist) {
759            if (!usePeriodicBoundaryConditions_)
760              Mat3x3d bbox = thermo->getBoundingBox();
761 <          neighborList = fDecomp_->buildNeighborList();
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();
765 –        rCutSq = cuts.second;
778  
779          if (rgrpsq < rCutSq) {
768 –          idat.rcut = &cuts.first;
780            if (iLoop == PAIR_LOOP) {
781              vij = 0.0;
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 822 | 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 918 | 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 938 | Line 956 | namespace OpenMD {
956      curSnapshot->setLongRangePotential(longRangePotential);
957      
958      curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
959 <                                         *(fDecomp_->getExcludedPotential()));
959 >                                       *(fDecomp_->getExcludedPotential()));
960  
961    }
962  
945 –  
963    void ForceManager::postCalculation() {
964  
965      vector<Perturbation*>::iterator pi;
# Line 968 | 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);
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;
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) {
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;
1010 >        n_j = RealType(info_->getGlobalCountOfType(*j));
1011 >        rho_j = n_j / vol;
1012            
1013 <          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1013 >        LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1014  
1015 <          Elrc += n_i   * rho_j * LRI.first;
1016 <          Wlrc -= rho_i * rho_j * LRI.second;
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;
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);
1022 >        RealType lrp = curSnapshot->getLongRangePotential();
1023 >        curSnapshot->setLongRangePotential(lrp + Elrc);
1024 >        stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1025 >        curSnapshot->setStressTensor(stressTensor);
1026        */
1027      
1028      }

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