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root/OpenMD/trunk/src/brains/ForceManager.cpp
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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1915 by gezelter, Mon Jul 29 17:55:17 2013 UTC vs.
Revision 2047 by gezelter, Thu Dec 11 16:16:43 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 "perturbations/UniformGradient.hpp"
62   #include "parallel/ForceMatrixDecomposition.hpp"
63  
64   #include <cstdio>
# Line 394 | Line 395 | namespace OpenMD {
395      switcher_->setSwitch(rSwitch_, rCut_);
396    }
397  
397 –
398 –
399 –  
398    void ForceManager::initialize() {
399  
400      if (!info_->isTopologyDone()) {
# Line 405 | Line 403 | namespace OpenMD {
403        interactionMan_->setSimInfo(info_);
404        interactionMan_->initialize();
405  
406 <      // We want to delay the cutoffs until after the interaction
407 <      // manager has set up the atom-atom interactions so that we can
408 <      // query them for suggested cutoff values
406 >      //! We want to delay the cutoffs until after the interaction
407 >      //! manager has set up the atom-atom interactions so that we can
408 >      //! query them for suggested cutoff values
409        setupCutoffs();
410  
411        info_->prepareTopology();      
# Line 417 | Line 415 | namespace OpenMD {
415        if (doHeatFlux_) doParticlePot_ = true;
416  
417        doElectricField_ = info_->getSimParams()->getOutputElectricField();
418 +      doSitePotential_ = info_->getSimParams()->getOutputSitePotential();
419    
420      }
421  
422      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
423      
424 <    // Force fields can set options on how to scale van der Waals and
425 <    // electrostatic interactions for atoms connected via bonds, bends
426 <    // and torsions in this case the topological distance between
427 <    // atoms is:
428 <    // 0 = topologically unconnected
429 <    // 1 = bonded together
430 <    // 2 = connected via a bend
431 <    // 3 = connected via a torsion
424 >    //! Force fields can set options on how to scale van der Waals and
425 >    //! electrostatic interactions for atoms connected via bonds, bends
426 >    //! and torsions in this case the topological distance between
427 >    //! atoms is:
428 >    //! 0 = topologically unconnected
429 >    //! 1 = bonded together
430 >    //! 2 = connected via a bend
431 >    //! 3 = connected via a torsion
432      
433      vdwScale_.reserve(4);
434      fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
# Line 447 | Line 446 | namespace OpenMD {
446      electrostaticScale_[2] = fopts.getelectrostatic13scale();
447      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
448      
449 <    if (info_->getSimParams()->haveElectricField()) {
450 <      ElectricField* eField = new ElectricField(info_);
449 >    if (info_->getSimParams()->haveUniformField()) {
450 >      UniformField* eField = new UniformField(info_);
451        perturbations_.push_back(eField);
452      }
453 <
453 >    if (info_->getSimParams()->haveUniformGradientStrength() ||
454 >        info_->getSimParams()->haveUniformGradientDirection1() ||
455 >        info_->getSimParams()->haveUniformGradientDirection2() ) {
456 >      UniformGradient* eGrad = new UniformGradient(info_);
457 >      perturbations_.push_back(eGrad);
458 >    }
459 >    
460      usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
461      
462      fDecomp_->distributeInitialData();
# Line 637 | Line 642 | namespace OpenMD {
642      // Collect from all nodes.  This should eventually be moved into a
643      // SystemDecomposition, but this is a better place than in
644      // Thermo to do the collection.
645 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
646 <                              MPI::SUM);
647 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
648 <                              MPI::SUM);
649 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
650 <                              MPI::REALTYPE, MPI::SUM);
651 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
652 <                              MPI::REALTYPE, MPI::SUM);
645 >
646 >    MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
647 >                  MPI_SUM, MPI_COMM_WORLD);
648 >    MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
649 >                  MPI_SUM, MPI_COMM_WORLD);
650 >    MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
651 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
652 >    MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
653 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
654   #endif
655  
656      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
# Line 666 | Line 672 | namespace OpenMD {
672      DataStorage* config = &(curSnapshot->atomData);
673      DataStorage* cgConfig = &(curSnapshot->cgData);
674  
675 +
676      //calculate the center of mass of cutoff group
677  
678      SimInfo::MoleculeIterator mi;
# Line 709 | Line 716 | namespace OpenMD {
716      RealType dVdFQ1(0.0);
717      RealType dVdFQ2(0.0);
718      potVec longRangePotential(0.0);
719 +    RealType reciprocalPotential(0.0);
720      potVec workPot(0.0);
721      potVec exPot(0.0);
722      Vector3d eField1(0.0);
723      Vector3d eField2(0.0);
724 +    RealType sPot1(0.0);
725 +    RealType sPot2(0.0);
726 +                  
727      vector<int>::iterator ia, jb;
728  
729      int loopStart, loopEnd;
# Line 728 | Line 739 | namespace OpenMD {
739      idat.dVdFQ1 = &dVdFQ1;
740      idat.dVdFQ2 = &dVdFQ2;
741      idat.eField1 = &eField1;
742 <    idat.eField2 = &eField2;  
742 >    idat.eField2 = &eField2;
743 >    idat.sPot1 = &sPot1;
744 >    idat.sPot2 = &sPot2;
745      idat.f1 = &f1;
746      idat.sw = &sw;
747      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
748 <    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
748 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE ||
749 >                         cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
750      idat.doParticlePot = doParticlePot_;
751      idat.doElectricField = doElectricField_;
752 +    idat.doSitePotential = doSitePotential_;
753      sdat.doParticlePot = doParticlePot_;
754      
755      loopEnd = PAIR_LOOP;
# Line 755 | Line 770 | namespace OpenMD {
770        }
771  
772        for (vector<pair<int, int> >::iterator it = neighborList_.begin();
773 <             it != neighborList_.end(); ++it) {
773 >           it != neighborList_.end(); ++it) {
774                  
775          cg1 = (*it).first;
776          cg2 = (*it).second;
# Line 769 | Line 784 | namespace OpenMD {
784          rgrpsq = d_grp.lengthSquare();
785  
786          if (rgrpsq < rCutSq) {
772 –
787            if (iLoop == PAIR_LOOP) {
788              vij = 0.0;
789              fij.zero();
790              eField1.zero();
791              eField2.zero();
792 +            sPot1 = 0.0;
793 +            sPot2 = 0.0;
794            }
795            
796            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
# Line 826 | Line 842 | namespace OpenMD {
842                
843                  r = sqrt( *(idat.r2) );
844                  idat.rij = &r;
845 <              
845 >
846                  if (iLoop == PREPAIR_LOOP) {
847                    interactionMan_->doPrePair(idat);
848                  } else {
# Line 926 | Line 942 | namespace OpenMD {
942      // collects pairwise information
943      fDecomp_->collectData();
944      if (cutoffMethod_ == EWALD_FULL) {
945 <      interactionMan_->doReciprocalSpaceSum();
945 >      interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
946 >
947 >      curSnapshot->setReciprocalPotential(reciprocalPotential);
948      }
949          
950      if (info_->requiresSelfCorrection()) {
# Line 945 | Line 963 | namespace OpenMD {
963      curSnapshot->setLongRangePotential(longRangePotential);
964      
965      curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
966 <                                         *(fDecomp_->getExcludedPotential()));
966 >                                       *(fDecomp_->getExcludedPotential()));
967  
968    }
969  
952 –  
970    void ForceManager::postCalculation() {
971  
972      vector<Perturbation*>::iterator pi;
# Line 975 | Line 992 | namespace OpenMD {
992      }
993      
994   #ifdef IS_MPI
995 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
996 <                              MPI::REALTYPE, MPI::SUM);
995 >    MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
996 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
997   #endif
998      curSnapshot->setStressTensor(stressTensor);
999      
1000      if (info_->getSimParams()->getUseLongRangeCorrections()) {
1001        /*
1002 <      RealType vol = curSnapshot->getVolume();
1003 <      RealType Elrc(0.0);
1004 <      RealType Wlrc(0.0);
1002 >        RealType vol = curSnapshot->getVolume();
1003 >        RealType Elrc(0.0);
1004 >        RealType Wlrc(0.0);
1005  
1006 <      set<AtomType*>::iterator i;
1007 <      set<AtomType*>::iterator j;
1006 >        set<AtomType*>::iterator i;
1007 >        set<AtomType*>::iterator j;
1008      
1009 <      RealType n_i, n_j;
1010 <      RealType rho_i, rho_j;
1011 <      pair<RealType, RealType> LRI;
1009 >        RealType n_i, n_j;
1010 >        RealType rho_i, rho_j;
1011 >        pair<RealType, RealType> LRI;
1012        
1013 <      for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
1013 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
1014          n_i = RealType(info_->getGlobalCountOfType(*i));
1015          rho_i = n_i /  vol;
1016          for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
1017 <          n_j = RealType(info_->getGlobalCountOfType(*j));
1018 <          rho_j = n_j / vol;
1017 >        n_j = RealType(info_->getGlobalCountOfType(*j));
1018 >        rho_j = n_j / vol;
1019            
1020 <          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1020 >        LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1021  
1022 <          Elrc += n_i   * rho_j * LRI.first;
1023 <          Wlrc -= rho_i * rho_j * LRI.second;
1022 >        Elrc += n_i   * rho_j * LRI.first;
1023 >        Wlrc -= rho_i * rho_j * LRI.second;
1024          }
1025 <      }
1026 <      Elrc *= 2.0 * NumericConstant::PI;
1027 <      Wlrc *= 2.0 * NumericConstant::PI;
1025 >        }
1026 >        Elrc *= 2.0 * NumericConstant::PI;
1027 >        Wlrc *= 2.0 * NumericConstant::PI;
1028  
1029 <      RealType lrp = curSnapshot->getLongRangePotential();
1030 <      curSnapshot->setLongRangePotential(lrp + Elrc);
1031 <      stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1032 <      curSnapshot->setStressTensor(stressTensor);
1029 >        RealType lrp = curSnapshot->getLongRangePotential();
1030 >        curSnapshot->setLongRangePotential(lrp + Elrc);
1031 >        stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1032 >        curSnapshot->setStressTensor(stressTensor);
1033        */
1034      
1035      }

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