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root/OpenMD/trunk/src/brains/ForceManager.cpp
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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1921 by gezelter, Thu Aug 1 18:23:07 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 393 | Line 393 | namespace OpenMD {
393      switcher_->setSwitchType(sft_);
394      switcher_->setSwitch(rSwitch_, rCut_);
395    }
396 –
397 –
396  
399 –  
397    void ForceManager::initialize() {
398  
399      if (!info_->isTopologyDone()) {
# Line 405 | 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 417 | 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 447 | 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 637 | 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 666 | 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 709 | Line 709 | namespace OpenMD {
709      RealType dVdFQ1(0.0);
710      RealType dVdFQ2(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;
# Line 728 | 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 755 | Line 763 | namespace OpenMD {
763        }
764  
765        for (vector<pair<int, int> >::iterator it = neighborList_.begin();
766 <             it != neighborList_.end(); ++it) {
766 >           it != neighborList_.end(); ++it) {
767                  
768          cg1 = (*it).first;
769          cg2 = (*it).second;
# Line 769 | Line 777 | namespace OpenMD {
777          rgrpsq = d_grp.lengthSquare();
778  
779          if (rgrpsq < rCutSq) {
772 –
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 826 | 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 926 | Line 935 | namespace OpenMD {
935      // collects pairwise information
936      fDecomp_->collectData();
937      if (cutoffMethod_ == EWALD_FULL) {
938 <      interactionMan_->doReciprocalSpaceSum(longRangePotential);
938 >      interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
939 >
940 >      curSnapshot->setReciprocalPotential(reciprocalPotential);
941      }
942          
943      if (info_->requiresSelfCorrection()) {
# Line 945 | Line 956 | namespace OpenMD {
956      curSnapshot->setLongRangePotential(longRangePotential);
957      
958      curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
959 <                                         *(fDecomp_->getExcludedPotential()));
959 >                                       *(fDecomp_->getExcludedPotential()));
960  
961    }
962  
# Line 974 | 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;
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;
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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