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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 2032 by jmichalk, Fri Oct 31 18:57:19 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 405 | Line 405 | namespace OpenMD {
405        interactionMan_->setSimInfo(info_);
406        interactionMan_->initialize();
407  
408 <      // We want to delay the cutoffs until after the interaction
409 <      // manager has set up the atom-atom interactions so that we can
410 <      // query them for suggested cutoff values
408 >      //! We want to delay the cutoffs until after the interaction
409 >      //! manager has set up the atom-atom interactions so that we can
410 >      //! query them for suggested cutoff values
411        setupCutoffs();
412  
413        info_->prepareTopology();      
# Line 417 | Line 417 | namespace OpenMD {
417        if (doHeatFlux_) doParticlePot_ = true;
418  
419        doElectricField_ = info_->getSimParams()->getOutputElectricField();
420 +      doSitePotential_ = info_->getSimParams()->getOutputSitePotential();
421    
422      }
423  
424      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
425      
426 <    // Force fields can set options on how to scale van der Waals and
427 <    // electrostatic interactions for atoms connected via bonds, bends
428 <    // and torsions in this case the topological distance between
429 <    // atoms is:
430 <    // 0 = topologically unconnected
431 <    // 1 = bonded together
432 <    // 2 = connected via a bend
433 <    // 3 = connected via a torsion
426 >    //! Force fields can set options on how to scale van der Waals and
427 >    //! electrostatic interactions for atoms connected via bonds, bends
428 >    //! and torsions in this case the topological distance between
429 >    //! atoms is:
430 >    //! 0 = topologically unconnected
431 >    //! 1 = bonded together
432 >    //! 2 = connected via a bend
433 >    //! 3 = connected via a torsion
434      
435      vdwScale_.reserve(4);
436      fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
# Line 447 | Line 448 | namespace OpenMD {
448      electrostaticScale_[2] = fopts.getelectrostatic13scale();
449      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
450      
451 <    if (info_->getSimParams()->haveElectricField()) {
452 <      ElectricField* eField = new ElectricField(info_);
451 >    if (info_->getSimParams()->haveUniformField()) {
452 >      UniformField* eField = new UniformField(info_);
453        perturbations_.push_back(eField);
454      }
455  
# Line 637 | Line 638 | namespace OpenMD {
638      // Collect from all nodes.  This should eventually be moved into a
639      // SystemDecomposition, but this is a better place than in
640      // Thermo to do the collection.
641 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
642 <                              MPI::SUM);
643 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
644 <                              MPI::SUM);
645 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
646 <                              MPI::REALTYPE, MPI::SUM);
647 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
648 <                              MPI::REALTYPE, MPI::SUM);
641 >
642 >    MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
643 >                  MPI_SUM, MPI_COMM_WORLD);
644 >    MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
645 >                  MPI_SUM, MPI_COMM_WORLD);
646 >    MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
647 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
648 >    MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
649 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
650   #endif
651  
652      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
# Line 666 | Line 668 | namespace OpenMD {
668      DataStorage* config = &(curSnapshot->atomData);
669      DataStorage* cgConfig = &(curSnapshot->cgData);
670  
671 +
672      //calculate the center of mass of cutoff group
673  
674      SimInfo::MoleculeIterator mi;
# Line 709 | Line 712 | namespace OpenMD {
712      RealType dVdFQ1(0.0);
713      RealType dVdFQ2(0.0);
714      potVec longRangePotential(0.0);
715 +    RealType reciprocalPotential(0.0);
716      potVec workPot(0.0);
717      potVec exPot(0.0);
718      Vector3d eField1(0.0);
719      Vector3d eField2(0.0);
720 +    RealType sPot1(0.0);
721 +    RealType sPot2(0.0);
722 +                  
723      vector<int>::iterator ia, jb;
724  
725      int loopStart, loopEnd;
# Line 728 | Line 735 | namespace OpenMD {
735      idat.dVdFQ1 = &dVdFQ1;
736      idat.dVdFQ2 = &dVdFQ2;
737      idat.eField1 = &eField1;
738 <    idat.eField2 = &eField2;  
738 >    idat.eField2 = &eField2;
739 >    idat.sPot1 = &sPot1;
740 >    idat.sPot2 = &sPot2;
741      idat.f1 = &f1;
742      idat.sw = &sw;
743      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
744      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
745      idat.doParticlePot = doParticlePot_;
746      idat.doElectricField = doElectricField_;
747 +    idat.doSitePotential = doSitePotential_;
748      sdat.doParticlePot = doParticlePot_;
749      
750      loopEnd = PAIR_LOOP;
# Line 769 | Line 779 | namespace OpenMD {
779          rgrpsq = d_grp.lengthSquare();
780  
781          if (rgrpsq < rCutSq) {
772 –
782            if (iLoop == PAIR_LOOP) {
783              vij = 0.0;
784              fij.zero();
785              eField1.zero();
786              eField2.zero();
787 +            sPot1 = 0.0;
788 +            sPot2 = 0.0;
789            }
790            
791            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
# Line 826 | Line 837 | namespace OpenMD {
837                
838                  r = sqrt( *(idat.r2) );
839                  idat.rij = &r;
840 <              
840 >
841                  if (iLoop == PREPAIR_LOOP) {
842                    interactionMan_->doPrePair(idat);
843                  } else {
# Line 926 | Line 937 | namespace OpenMD {
937      // collects pairwise information
938      fDecomp_->collectData();
939      if (cutoffMethod_ == EWALD_FULL) {
940 <      interactionMan_->doReciprocalSpaceSum();
940 >      interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
941 >
942 >      curSnapshot->setReciprocalPotential(reciprocalPotential);
943      }
944          
945      if (info_->requiresSelfCorrection()) {
# Line 949 | Line 962 | namespace OpenMD {
962  
963    }
964  
952 –  
965    void ForceManager::postCalculation() {
966  
967      vector<Perturbation*>::iterator pi;
# Line 975 | Line 987 | namespace OpenMD {
987      }
988      
989   #ifdef IS_MPI
990 <    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
991 <                              MPI::REALTYPE, MPI::SUM);
990 >    MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
991 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
992   #endif
993      curSnapshot->setStressTensor(stressTensor);
994      

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